Gibbs Recursive Sampler: finding transcription factor binding sites

Nucleic Acids Res. 2003 Jul 1;31(13):3580-5. doi: 10.1093/nar/gkg608.


The Gibbs Motif Sampler is a software package for locating common elements in collections of biopolymer sequences. In this paper we describe a new variation of the Gibbs Motif Sampler, the Gibbs Recursive Sampler, which has been developed specifically for locating multiple transcription factor binding sites for multiple transcription factors simultaneously in unaligned DNA sequences that may be heterogeneous in DNA composition. Here we describe the basic operation of the web-based version of this sampler. The sampler may be acces-sed at and at An online user guide is available at and at Solaris, Solaris.x86 and Linux versions of the sampler are available as stand-alone programs for academic and not-for-profit users. Commercial licenses are also available. The Gibbs Recursive Sampler is distributed in accordance with the ISCB level 0 guidelines and a requirement for citation of use in scientific publications.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Binding Sites
  • Genetic Variation
  • Internet
  • Markov Chains
  • Monte Carlo Method
  • Repetitive Sequences, Nucleic Acid
  • Sequence Analysis, DNA / methods*
  • Software*
  • Statistics, Nonparametric
  • Transcription Factors / metabolism*
  • Transcription Initiation Site
  • User-Computer Interface


  • Transcription Factors